Rise of the Dark Turtle
by Venka le fay
Summary: Three of the four turtles have been sent 20 years into the future. They find themselves in a future version of New York that is controlled by the Shredder. And the brother they have left behind has taken on a persona known as the Dark Turtle and hell bent on ending the Shredder once and for all.
1. Chapter 1

Rise of the Dark Turtle

I came up with this idea for a Turtles in time event on a thread I on the technodrome forums called "Episode Idea thread (Turtle Torture Edition)" I figured that if the Nick Show ever decided to use the Dark Turtle this would be a good way to do it.

As usual I don't own Ninja Turtles. TMNT is the brain child of Keven Eastman and Peter Laired. It is currently owned by Viacom and Nickelodeon, all rights reserved. I don't write this for any personal gain. Please support the official release.

* * *

"This is Commander Xever." Fishface spoke into his comlink. "I have the Dark Turtle cornered in an old warehouse there is nowhere he can run. Tonight he finally ends."

"Will you need back up?" Came a reply from the mutant soldier at the other end.

"No, I will suffice." Fishface insisted, his remaining eye looking at the entrance to the dockside warehouse. He sneered in triumph, after all these years the last of the Ninja Turtles would finally fall and the Shredder would finally hold control of the city and the world.

It had been twenty years, twenty glorious years since three of the four terrapin ninja had fallen in battle. The forth one had survived…running back to his sewer dwelling and merely delaying the inevitability of his demise.

Entering the darkened building the mutant scanned the gloom for any sign of movement. He knew the Turtle believed he had the upper hand...that he had the advantage.

"Come out boy," Fishface called into the darkness. "There is no where you can hide, no where you can run. I don't know how you've been so fortunate as to survive these past twenty years since your brothers have been destroyed. But your luck has just run out and the resistance will fall with you!"

He jumped out of the way as several Kunai came flying out of the darkness narrowly missing him. The mutant fish stumbled slightly as he landed, he wasn't as spry as he once been but he was still strong enough to take out this turtle.

"There is much I do find commendable about you, I will admit to that." The old fish said continuing to scan the darkness. "You have hampered our efforts to eliminate the resistance on numerous occasions, defeated scores of Foot Mutants and Soldiers. You've managed to silence the irksome sound of Zeck's voice…though it is a pity you didn't succeed in ending his life along with his precious voice box. You've even managed to take out my left eye."

"Do you ever stop talking Fishface?" A voice said from the shadows. A shuriken flew from the shadows on Xever's right. The flying metal star sliced though his cheek as he feinted out of its path. But he didn't care, it was a war wound and it was something he could proudly display as something he earned in the fight in which he took down the Dark Turtle. Xever also marked out the shape of a mutant turtle as it sprinted further into the shadows. This was the costly mistake the mutant fish had waited for.

Reaching into a pouch he had with them he pulled out one of Stockman's more useful inventions, a light bomb. Similar to flash bang it would produce a sudden blast of light. However the light would last a total of twenty minutes causing this deadly game of cat and mouse to be reversed. When that happened it would be the Turtle who will be fighting for his life.

Throwing it into the air it detonated illuminating the warehouse in bright white light. Fishface blinked his single eye as it adjusted to the sudden light. Fortunately the Turtle would be disoriented as well, so he wasn't in immediate danger.

"Come on out, Turtle." Xever said. "If you surrender…perhaps I let you live, yes? Perhaps you ask for pardon in exchange for your loyalty to Master Shredder."

"I don't pledge loyalty to cowards." The Dark Turtle answered from somewhere off to Xever's left. Pulling out his butterfly knives the mutant fish stalked towards the voice. At that moment there was a sharp thrum followed by an even sharper pain as an arrow sprouted from Fishfaces chest. The wound was serious and if not tended to it would be fatal. He could feel the arrow had pierced a lung making it hard to breathe even with his water tanks. The strike had come from behind him. At one he rounded before a huge morning star descended from the rafters destroying one of the water tanks on Fishface's back.

The mutant fish fell over gasping as he tried to breath. A figure appeared before him, completely dressed in black, even his face was covered in by a black hooded mask. The Dark Turtle simply regarded the dying mutant neither in anger nor in pity, but calm indifference.

"Mer…mercy." Fishface gasped.

"The same mercy you showed all the innocent people you and the rest of the Foot have mutated, terrorized, or killed?" The Dark Turtle coldly asked.

"No…please." Fishface gasped. "Ple…ease help…save me." Calmly the Dark Turtle moved towards the door of the warehouse. Pulling a smart phone shaped device from one of his belt pouches he paused a moment to adjust it. While the Turtles back was turned, Fishface slowly reached for the one of his butterfly knives. He may die, but the turtle would die with him.

Reaching back his arm he was going to toss the blade, aiming for the turtles carotid artery when the Dark Turtle turned back to face him.

"Give my regards to Mr. Murakami, Pigeon Pete, and Kirby O'Neil!" He said as he dropped the device to the ground and sent it skidding towards the mutant fish. Fishface's blurring eyes widened in alarm as he saw the digital display counting down from 15…14…13. He didn't hear or see the Dark Turtle running from the scene. He could only watch the seconds that counted down to a concussion that sounded for at least five city blocks.

The blast engulfed the warehouse sending up a firey blaze into the night sky. The Dark Turtle regarded it for a time before his gaze traveled the blood red lights of the city. It felt like an eternity ago that he and his brothers had first crawled out of their sewer dwelling for the first time and witnessing the sky scrapers rising like big silver towers in the distance. But ever since the Shredder had taken over…the city had become a black ugly dread fortress, a fortress that he was determined to see fall.

"I'm coming for you Shredder." The Dark Turtle snarled venomously. "Mark my words…I will end you and your reign of terror."

* * *

Mean while in the heart of the city, a light appeared depositing three mutant figures that had not been seen for twenty years. Glancing about they didn't question where they were…but when.


	2. Chapter 2

[20 years earlier]

"Oooo, Oooo, guys!" Mikey said. "When we get back from spying on Shredder, let's order some Antonio's! There is a toping combination I wanted to try, Salami, pancetta, green onions and chocolate fudge."

"Can't you guys eat normal kinds of pizza for once like Italian sausage and basil?" Casey asked.

"Are you kidding you can put anything and everything on a pizza!" Mikey said. "The pizza crust is just a blank canvas and its toppings are what make it great."

"It's better not to encourage him." April said as she placed her war fan in her pocket. "But I could go for some Murakami's Pizza Gyoza later."

"Time to roll out guys." Leo said. "Remember we are not engaging Shredder or his mutants, we are just observe what he's planning for now."

The four turtles and two humans went to their battle stations. As they climbed into the party wagon, Casey smugly grinning at Donnie over the fact that April was riding in the front seat while the other was forced to sit in the back. Starting the van, they took off into the city night. The city was still recovering from the defeat of the Kraang weeks ago,with them gone that fortunately did slow down the Shredder somewhat but it didn't cripple his efforts.

The knowledge that Shredder had been developing a mind control serum bothered them all because of how inclusive it was. The very city that they had been fighting to protect could be completely turned against them. Heck their own brothers could be turned against one another and none of them wanted to fight any of them…not as an enemy. The only way to prevent that was to make sure that all attempts were thwarted.

The four brothers and two humans climbed to the roof top as Donnie fidgeted with an app on his t-phone. Across the street from them was the abandoned cathedral that Shredder used as his lair and seat of power.

"I've released a number of Spy Roaches into the building so we should have audio and visual soon." Donnie filled in the three Turtles arrived as his t-phone continued to put each of the spy roaches online until the visual of the Shredder's throne room came into focus.

"…are almost complete mazzzter." Stockman buzzed over the feed. The other turtles gathered and two humans gathered around Donatello as the one of the spy roaches zoomed in on the conversation. Shredder was seated on his throne with Tiger Claw standing on his left hand side. Stockman was kneeling before the dais like a simpering insect waiting to be devoured by a hungry spider.

"Good…" Shredder intoned. "Now what efforts have you made to restore my daughter?"

"Karai…He has Karai?!" Leo asked in a panicking tone.

"Shhhh…" Donnie hissed, though he did throw Leo a glance in quiet understanding of his brother's distress

"Well zzzzz Mazzter….there has been zzzsome minor….zzzzsetbacks." Stockman said.

"SETBACKS!" The Shredder roared angrily. "You were to restore her humanity!"

"I've been trying mazzter…" Stockman whined.

"Good luck with that Buzzkill." Mikey snorted which Casey agreed with a smirk.

"Pray you find a way or you find some who can…my patience wears thin." Shredder growled. Leo and Raph instinctively huddled closer to Donatello and April. If Shredder had Karai, that meant they had to find a way to restore her fast...before the Shredder learned Donnie could reverse mutations or that April's DNA was key. Baxter got up and left the room returning to his lab.

"We can't leave…not until we've freed Karai." Leo said.

"Get off it Leo, we have more things to worry about then saving your girl friend." Raph said.

"I'm not saving my girlfriend, I'm saving Splinter's daughter." Leo shot back.

"Who also happens to be your love interest?" Raph needled.

"Baxter's probably keeping her in his lab…" Donnie jumped in before things got ugly.

"Well, well, well." A thickly accented voice said. "It seems we have small infestation of turtles." Turning the six teens found themselves faced with the newest members of Shredder's hench mutants.

"Yeehee Christmas has come early." A mutant warthog with a purple Mohawk said from behind the bulky mutant rino that had just spoken.

"Oh no," Mikey complained. "It's Rocksteady and Bebop!"

"How many times do I have to tell you not to call me "BEBOP!" The Warthog mutant yelled. "I seriously hate that name."

"It seems you two have your uses after all" Rahzar laughed as he and Fishface appeared surrounding them against the edge of the roof.

"Turtle Soup for everybody!" Fishface smirked.

"While you're making the soup I want them to watch as I feast on the humans." Rahzar said as he stalked forward. "Starting with the girl." Donnie stepped defensively in front of April as all four the Turtles and the two humans all drew their weapons.

However before the fight began the sky was cleaved in two as a bright lightning bolt struck the roof top and created a portal of blue light no one had ever seen before and began so suck in everything in its path which included Leo, Raph, and Mikey.

"Guys!" Was all a horrified Donatello could say as the portal closed and disappeared taking his brothers with it, leaving nothing but a scorch mark behind.

* * *

[20 years later]

A spark followed by a beam of blue white light appeared before spitting the three turtles out onto the roof top. Dazed and confused about what had just happened they shook their heads to clear them.

"Did either of you guys get the number of the vacuum cleaner that just hit me?" Raph groused.

"Don't talk to me…I'm so dizzy I think I'm going to hurl." Mikey said before rushing to the side of the roof and began heaving his guts.

"I don't see Donnie with us…he was probably left behind." Leo said as he took stock of the brothers who were with them.

"Yeah…April and Casey too." Raph said. "But a better question would be where are we?"

"No…" Mikey said as he recovered. "The better question would be 'when are we?' He pointed out towards the island where the statue of liberty always stood. However instead of the famed statue there was a large metal statue of the Shredder, one armed raised the blades of his gauntlets extended as though he were about to bring them down upon whoever dared enter the New York Harbor.

Around them the facades of the familiar buildings were all black as red lights shown through each window. Each building was also spikey and twisted into some ghastly asianesk fashion. And the Foot Clan insignia was everywhere. On the buildings, on buses, on flags and banners.

"Well wherever we are or whenever we are…one thing is for sure, the Shredders been busy." Raph commented.

* * *

Climbing down to the street the three Turtles stuck to the shadows. It didn't take long for them to notice most of the inhabitants were mutated into various animals, reptiles, and amphibians. All of them dressed in black and wearing the Foot Insignia somewhere on their clothing.

"Obey Emperor Shredder!" Tiger Claw's voice boomed out. "Resistance is death…" The monitors and screens around the city also displayed known resistance members. Raph's eyes widened in surprised as Slashes face filled the large Time Square screen followed by an older Dr. Rockwell.

"Attention citizens of District 10." Rahzar's voice said over a loud speaker as the image of a large mutant turtle like figure dressed head to toe in black ninja garb appeared on the screen. "Be on the lookout for a criminal known as the Dark Turtle. He is wanted for various crimes around the city including the death of numerous Foot Loyalists and most recently the murder of Commander Xever..."

"I can so come up with a better name then Dark Turtle." Mikey griped.

"Now's not the time, Mikey." Leo said as he looked about. No one was paying them any mind so he decided to risk stepping out into the street,

"There is Knight of Turtles, Terrapin Darkness, Night Watcher, Shelled Terror." Mikey continued to complain as he listed off the names he felt were better then "The Dark Turtle."

"Seriously just let it go." Raph growled. "Though that Night Watcher name sounds cool." Unfortunately the conversation attracted the attention of a mutant lion and a mutant ferret. Both of them were dresses in the same black uniformed attire as everyone else.

"Hey, where's your Foot garb!" The Mutant Lion called out causing the three turtles freeze in their tracks.

"Oh ah…we are new to the city." Leo said. "So we aren't familiar with everything yet."

"Yeah were from…from Tokyo." Mikey said making a show of bowing. "English very choppy Lion-san."

"Them Turtles are lying, Arny." The ferret mutant hissed. "Tokyo hasn't existed for the past five years…Everyone knows it's called District #1 now and the capital seat of Emperor Shredder empire."

"I thought I smelled resistance scum, Buddy." The mutant lion agreed.

"Really, and I thought the smell of scum was from you two." Raph said as he pulled out his sai. "Care to make my day you shaggy excuse for a house cat?"

"No, run." A female falcon mutant yelled from overhead earning more attention from the populous of the city. "Arny and Buddy are bounty hunters for the Foot Clan."

"But why are..?" Raph asked the falcon.

"Just run!" She yelled as she flew off. The three turtles didn't question it and took off racing down the street.

"STOP THEM!" Arny roared as he raced after. "THOSE TURTLES ARE RESISTANCE! The three turtles didn't look back or stop they ran as though their lives depended on it. The mutants around them trying to grab them, restrain them, or block them from escape. The crowed thickened hemming them all in when suddenly they eyes of all the mutants including Arny and Buddy started to glow a cyan blue color before they dispersed and seemed to forget all about the three mutant Turtles.

"This way…" The female mutant said as she beckoned them down an ally way before stopping and allowing to get the Turtles to get a good look at her. She had deep reddish brown hair that rested just above her shoulders. Her skin was lightly covered in deep gingerbread brown feathers though the there was a butterfly mask of white flesh around her eyes and even more around white flesh around her bare thighs which were covered by a pair of brown tights. She was dressed in a long sleeved and short skirted rich brown dress which was tan colored around her bust chest and waist. Her feet were covered in gold boots that ascended to the calves of her legs. Out of her back were a pair large birds that made her appear more angelic then human. Though the bird beak that served as her nose and mouth said other wise.

"Thanks for saving us and all." Raph said as he caught his breath. "But who are you?"

"My name is Faith…" The falcon mutant said. "Or that's what it is now…I am a member of the resistance. You wouldn't remember me given how I have changed so much since you saw me last. But I was a six year old child when you met me and had tea with me Mr. Turtle." Faith smiled at Leo.

"You're the…" Leo gasped in surprise.

"Yes," Faith said with a smile. "Or more rather…I used to be."

"But how did…why are?" Leo flustered asked.

"It's a long story…but basically when the Shredder took over the city he decreed every child was to be taught how to fight and used weapons in addition to the usual reading, writing, and mathematics. I was a poor student in that regard as I didn't have any interest in martial arts. The people who had no potential to be Foot Soldiers were forcibly mutated. Of them it only a fraction were able to retain their some level their humanity, while others lost their minds to their mutations and were locked away…never to be seen again. My father was one of those people.

"I was mutated into this creature you see before you and trained to be part of the Shredder's Raptor Guard." Faith continued.

"Oh wow, I love Jurassic park." Mikey said earning a swat in the back of the head from Raph.

"But we remember Shredder had been developing a mind control serum." Raph said.

"He succeeded." Faith answered. "It was given to you through food during training and piped into the water supply of the training centers. That's how I became part of the resistance. Several members arrived and saved as many people as they could…I was one of the ones they liberated. For about two weeks I was sequestered in an old hotel room, gradually my mind cleared from seeing the Shredder as someone who should be blindly followed and respected and saw him as the monster we truly was." The formerly human girl paused and brushed away tears. "I wanted him to pay for what he had done to me, that horrible man ruined my life."

"Don't cry Faith," Mikey comforted. "We'll make him pay for what he's done."

"This world still bothers me." Leo said. "I don't even know how we got here or how we would even get back to prevent any of this from happening."

"Maybe the leaders of the resistance would know," Faith suggested. "Follow me…"

* * *

"The Dark Turtle watched through his telescope as Bebop and Rocksteady rode down the street in their van. Neither the Russian Rino nor the Mute Warthog knew what sat beneath their vehicle. In his hand he held a trigger…his thumb over the button. As the two mutants rode into an empty intersection he pressed the trigger button before the van erupted into a ball of flames.

There were screams of surprise and fright from the people on the street as it happened. Rocksteady lumbered out of the burning wreckage, his body bloody and burnt as he yelled for help. The larger horn on his nose had broken off in the explosion and both of his eyes were just empty bloody sockets. But it wasn't likely the Shredder would let him live to see much beyond that. The Shredder hated any form of weakness…so anyone who was disabled, sick, and infirm was euthanized while people who were severally injured were shot on scene.

This only left Rahzar and Tiger Claw standing in his way, and the Shredder would be returning from District #1 that very night. Before this week was through everything would be as it should be ….and his brothers would be avenged.

"There you are." A female voice said from behind him. The Dark Turtle didn't turn to her or answer. The dark haired woman stepped to his side and looked on as the flashing lights of the police vehicles arrived at the scene to assess the damages and kill off anyone that was too wounded to leave the scene. A sharp gunshot filled the air signifying the end of Rocksteady.

"Father often asks about you." She said. "He worries."

"I'm doing what needs to be done…" The Dark Turtle growled. "What should have been done."

"Believe me I understand." The Dark Haired woman said. "But even after all this time, you must know that the Shredder is not someone you can defeat on your own. Remember I went after him on my own and I paid a hefty price for it. But it was thanks to you and O'Neil that I was able to be restored. She restored my mind and your retromutagen restored my humanity."

"You're still able to turn into a snake." The Darkturtle said as if stating a fact.

"Yes…"The dark haired woman said. "But I am also able to control when I wish to be Karai and when I wish to be Kiba rather feel like I am losing myself to my snake form even when I am able to be human. But that's beside the point... the fact is the rest of us want to be here for you Donatello, but you have to let us."


	3. Chapter 3

"You told us about what happened to you when the Shredder had been taking over," Leo inquired of Faith. "But what happened to this city…to the world after we um…were sent to this time."

"It is unfortunately not safe to talk out here in the open." A familiar intellectual voice said Dr. Rockwell slipped out of the shadows. Beside him was the hulking frame of Slash. Both of them aged much over the years. Rockwell's face sagged and his brown fur was tinged with gray, while Slashes rich blueish-green scales had taken on a somewhat faded hue.

"Slash?" Raph said in surprise.

"Dr. Rockwell?" Leo also said.

"Thank you for your assistance with saving them from the crowd, Dr." Faith said earning a brief but appreciative smile from the elderly psychic ape.

"But where's Pete….and Leatherhead?" Mikey asked as he noticed two of the mutanimals were missing. Both Slash and Rockwell glanced at one another before closing their eyes in sorrow.

"Pete was killed by Fishface in a raid upon a Foot Clan training facility." Slash said sadly. "Leatherhead…he died of old age three years ago." The look on Mikey's face said it all…part of it sadness that his gator friend was no longer around. And part of it confusion as to why he would be dead of old age so soon, then he remembered. That one time long ago where they had found and recovered Leatherhead when they went to Dimension X for the first time.

They had found him much older than the young alligator that had heroically dragged Trag back into Dimension X. Mikey was confused as to why his friend had grown so old, it had been at least a handful of months in their dimension since they had seen him.

"_It's the time-differential, Mikey._" Donnie had calmly said with some degree of sadness. That one statement had summed up everything in that moment. Leatherhead also agreed this was the case and imparted that he had been in Dimention X and fighting the Kraang for decades.

"No…" Mikey whimpered as tears began to seep from his eyes. "I…I never got to tell him goodbye." Raph put a calming arm around his baby brothers shoulders in an attempt at comfort.

"How…how long have we been gone?" Leo asked cautiously. He knew he wouldn't like the answer but he needed to know. How long had the world been left in jeopardy while they had traveled through time and space to this horrible future?

"All will be revealed once we reach headquarters." Faith answered. "As Dr. Rockwell has said…It's not safe to talk in the opening…the spiders are always listening."

* * *

Rockwell's words couldn't have been truer as Tigerclaw stood in wait beside the limo as the Shredder's private jet plane landed at District #10's municipal airport. It was a large black 747 painted with red slash marks and the Foot Insignia stamped on the tail. The cargo bay door opened and Shredder trooped out flanked by a mutant black panther and a mutant cougar, who had dubbed themselves with the names of Talon and Fang. Both of mutant cats war identical foot uniforms, Black Trousers and sleeveless muscle shirts with the Foot insignia embroidered on the front pocket area of their chest.

The mutant tiger and the members of the Raptor Guard that stood with him all stood at attention. Despite the two decades that have passed, the Shredder was still formidable and dangerous.

"Master Shredder" Tiger Claw greeted.

"So is it true…?!" Shredder growled back.

"Yes, Master." Tiger Claw confirmed. "Xever has been destroyed; Steranko and Zeck were killed as well."

"It matters not." Shredder said with no remorse as he climbed into the limo, Tiger Claw climbing in afterwards. "Though that blasted turtle has proven to be quite an annoyance. I want him captured so Splinter can watch as the last of his sons dies."

"There has been word the other three Turtles have reappeared." Tiger Claw informed.

"WHAT?!" Shredder snarled.

"I find it hard to believe myself." Tiger Claw admitted. "But it's possible that whatever caused them to disappear may have sent them forward in time."

"Then make sure they don't return to back to the time they left." Shredder snarled angrily. "I have worked too hard to gain control of this world. I won't my efforts to be wasted."

"What of your cub?" Tiger Claw said. "She is a traitor and has joined the resistance."

"She is dead to me!" Shredder growled lowly in his throat. "I had hoped to control her…but if she cannot obey me…she will suffer at my hand like all the resistance."


	4. Chapter 4

"Halt!" A bat mutant called out in an anally retentive and nasally voice as he flew down to meet them. The mutant was about half the size of Mike as he flapped in place and dressed in nothing but a red scarf with a pair of spectacles perched on his snout "Who are you, what is your purpose."

"Ooo ooo," Mikey said excitedly. "I have the perfect name for this guy."

"The names Dimitri Tiberius Bat," The bat mutant sniffed distastefully at the young mutant. "I don't require names from mutants of your variety."

"Awww and I was going to call you Night Wing," Mikey whined.

"Should have gone with Wingnut." Raph whispered to his younger brother.

"Don't mind him…" Faith said sympathetically. "Turtles, meet Demitri, he's our look out."

"Look out…?!" Demitri complained in a nasally whine. "I am no measly look out. I am a night guard and spy, and the greatest in all the resistance."

"Oh, right…..my mistake." Faith said, with a somewhat pained expression. "Anyway, could you let us through?"

"Wait, wait, wait," Demitri groused. "I know, you, Slash, and Rockwell are authorized…but these Turtles aren't. How do you know they can be trusted?"

"Believe me," Faith said with some irritation. "They can be trusted…they are old friends."

"I'll determine if they should be trusted or not!" Dimitri insisted. "First show me your documentation papers!" A large green fist smashed into Dimitri's face sending the bat flying into the brick wall behind him. Stalking up Slash pulled something from off of Dimitri's belt and pressed button on it revealing the hidden entrance way that Donnie had installed for the ShellRaiser years ago.

"Follow me," Faith said unabashedly as the group entered the sewers, Slash followed dragging Dimitri with him before closing the hatch and dumping the mutant bat and the remote unceremoniously in a corner of the sewers.

"To think we lost Pete, just for this guy." Slash grumbled.

"Don't bother explaining…I don't want to know." Raph growled. "Let's get to where were going."

"Hey dudes, doesn't this place feel kinda familiar?" Mikey commented as he looked about the tunnel they were traveling down until they saw a familiar set of turnstiles up ahead.

"It's the lair!" Mikey crowed as they approached, however their home had greatly changed over the decades. Bunk beds were strewn everywhere, there were also numerous humans and mutants milling about, some polishing guns and other weapons. Others had set up a card table and were well into a poker game. An occasional head looked up at them in curiosity but otherwise took no notice.

"What happened to the place?" Raph inquired and narrowly avoided being run into by a small mutant child that was running about like he didn't have a care in the world.

"This one of the resistance strong holds," Slash explained. "There are ten resistance groups in the city, this group calls itself "The Ghosts" because we are the ghosts of the world that once was."

"I see" Leo said as he looked around as Faith escorted them to the Dojo before she left their side. The tree in the training room sadly was gone, but towards one wall was a table. A man and woman, both in their late thirties were looking over maps of the city and plans and softly talking to one another.

The man was dressed completely in black, black pants, black utility belt, black tank top. A black bandana covered to thirds of his face. Beside him was a woman with fiery colored hair. Like the man beside her she also wore black. However underneath the black hooded sweat shirt she wore was a butter yellow long sleeved t-shirt.

The turtles took an intake of breath at the sight of the man and woman, as they knew instantly who they were, Casey Jones and April O'Neil. The man turned to them as they all entered, his eyes widening in surprise before taping the woman's shoulder.

"Leo?..." April asked in aww. Leo noted that her voice had taken on a rasp as though damage was done to her throat. "Mikey…Raph?"

"Hey April," Mikey said offering a small smile.

"Guys!" April said running up and throwing her arms around Leo's neck. Mikey wrapped his arms around April around both Leo and April.

"It's been forever." Casey responded as he pulled down the bandana that covered his face. Casey's face still had the same impish smile he had from years before. Missing front teeth and all, the only thing that was difference was that a soul patch had grown in under his bottom lip.

"I wish I could say the same." Raph said as he playfully punched Casey's shoulder in greeting.

"My sons…?" A voice said from the opposite site of the Dojo. Standing in the door way of his room, was none other than Splinter. The elder rat had grown older and frailer over the passing years. The patches of rich brown fur had dulled and become flecked with gray. Standing beside him was Karai. Her form was human once more. Gone was the Foot Kunoichi attire she always wore, but a pair of black capris. Her shirt was also black but the long sleeves were vertical stripes of black and hamato clan crimson. She also wore a crimson bolero jacket with the Hamato clan crest emblazoned in white on her shoulders.

"Master Splinter!" All three turtles said. April moved aside to allow the three turtles to greet their father. Splinter's arms enfolded around his three sons welcoming them back to his arms.

"I had thought you three were lost forever." He said as he embraced his missing sons. Karai smiled warmly at the four of them as she went to stand with Casey and April. Mikey's smile started to fade as he noticed that one person who should be with them hadn't appeared yet.

"Is Donnie going to be here soon?" He asked. Splinter looked troubled at this innocent question.

"Yeah, where is Donnie anyway?" Raph asked, also noting that this reunion was not complete until his immediate younger brother was with them.

"He's out…" Karai said simply. April and Casey also looked as though they were having a hard time trying to tell the other turtles.

"Out helping this Dark Turtle character?" Leo supplied. He hoped that was the case, because he had a sinking feeling from the moment he saw that image that he knew who was hiding underneath that black Ninja Garb.

"Leo…" April rasped as she came forward. "Donnie is the Dark Turtle."

* * *

**AN: I wanted to get this chapter out by my 33****rd**** b-day, which is today. **

**Big hug and thank you to: , Turtle Lover101, PhGim.7, BrownEyedBirdie, Anonymous Guest, kooksandwally4eva, BlueFireReturns, TMNTPRO15, slynaxx, Tuskafel , yukio87, GirlRobin, and Mileena Cage BR**

**It's people like you who keep me writing. You guys rock. ****J**


	5. Chapter 5

The Dark Turtle watched through a telescope as Shredder left his limo and entered Foot Headquarters, Shredder's seat of power in this city. Years ago, this building had been known as TCRI and had been the strong hold of the Kraang. Shredder claimed the empty building as a his own making it his new lair as he began to rule the city with an iron fist.

"Attention citizens of Foot Island, District #10." Rahzar's voice growled over a loud speaker. "Be on the lookout for a mutant calling themselves the Dark Turtle. He's a wanted fugitive associated with the resistance. His crimes include interfering in and/or sabotaging city projects, destruction of Foot Clan property, abducting recruits from training facilities, involvement with resistance groups including but not limited to "The Ghosts" and the "White Snakes", Inspiring riots and overall chaos, and the orchestrating murder of several Foot Clan operatives including: Xever Montes, Ivan Steranko, and Anton Zeck. Because of this mutant's crimes, Emperor Shredder has raised his bounty and decreed that $10,000 crimson yuan's will go to anyone who does their duty and brings the Dark Turtle to justice.

The Dark Turtle listened to the report with vague attention. Ten-thousand crimson yuan's was roughly the equivalent of a million U.S. dollars back before the Shredder took over. This meant the Shredder was certainly concerned about his pending downfall. However this also meant that he had to inform Karai so she can convey the news to the Ghosts and her own resistance group the "White Snakes". There were members of the resistance who would sell out their own mothers for that amount of money. A lone mutant turtle wouldn't be that much of a loss in their book at least. For April, Casey, and Karai this meant observing their group members would anyone who would sell out one of their own. Not a pleasant task when you needed all the warriors you could get.

With a sigh he looked up at the starless, smoggy sky and softly whispered. "Leo, Raph, Mikey…Where ever you are, please know everything I've done. And everything I do is for you, and I pray that you will learn to forgive me for what I have become."

* * *

Leo could feel his stomach drop in shock as April said those words. His kind hearted, annoyingly intellectual brother was a wanted fugitive. Being part of the resistance he supposed that was possible But this still wasn't the Donatello he had known. The Donnie he remembered loathed the idea of taking a life…even the life of an enemy. What had happened to change him in this way….why had this happened?

"How…how long have we…" he asked. Distress filling his voice as he re-asked his earlier question, he knew he wouldn't like the answer but he had to know. He had to hear how long it had been since the three of them were pulled into that vortex.

"It's been…It's been twenty years, my son." Splinter answered. Raph gave an intake of breath, while Mikey gave a small whimper, Leo on the other hand felt like he was going to be sick to his stomach. It was little more than an hour ago that he had been standing with his brothers, April and Casey, and now three of them were here in the future while the rest of them were left behind to suffer twenty years under the Shredder's rule.

"What…what happened?" Leo asked in hardly more than whisper. "How did all this happen?"

"Are you sure you want to know?" Karai asked cautiously.

"Yes!" Leo practically yelled. He breathed a bit to help calm himself before he continued. "Yes, I need to know. I don't know what happened over the twenty years we have been missing or even how to fix what the Shredder has done. But what I do know is one of my brothers is out there in the city and he's fighting for more than just this city. He's fighting for his sanity. Anything that concerns one of us, concerns the rest of us and we can't help him if we don't know what he's gone through."

"It's a long story." Casey said.

"We still deserve to know." Raph said.

"Right." Karai answered. "You all might want to sit down."

* * *

[20 years ago.]

"Guys!" Donnie cried out for his brothers in horrified anguish as the time vortex closed and disappeared leaving nothing but a scorch mark on the roof to mark where it had happened. Rahzar, Rocksteady,Bebop, and Fishface were all temporarily disoriented by what had happened. Knowing Donnie was more at a disadvantage without his brothers, Casey at once grabbed the mutant turtle and pulled him to the edge of the roof.

"Come on, Red!" Casey shouted as the three of them descended the roof towards the safety of the sewers. "Let's get Donnie outta here!" April didn't argue as she jumped through the grate to the dark, malodorous labyrinthine tunnels. Both slinging one of Donnie's arms over their shoulders, they rushed as far away as they could to prevent themselves from being followed through the tunnels. The one question on the minds of both teens was "What happened to the others? And how were they going to tell Splinter?"

* * *

[79th Level of Null Space]

A short man dressed in a robe looked down at the time staff where it lay cracked and broken on the floor. The staff was tall and bore an hour glass on the top of it. Several grains of silvery sand slowly poured out of the large crack in the hour glass. Beside him stood a tall young woman wearing a silvery blue leotard covered with various clocks around her waist.

"Oops." The girl said sheepishly.

"Oops?!" The man turned to her incredulously. "Is that all you can say, Renet?! Just oops?! I have told you countless times the Time Staff is not a toy."

"I'm sorry, Lord Simultaneous." Renet pleaded. "I just wanted the six months of dusting duty to go by quicker."

"You'll lucky if I only give you six years of dusting duty after this." Lord Simultaneous growled. "Thanks to you, the time staff has been broken. I have to get it fixed before I can even hope to repair any damages you have caused to the times stream, now make yourself useful and see who was affected by all this."

"Yes sir," Renet answered and set to work on her task.


	6. Chapter 6

[20 years prior]

Splinter breathed and out centering himself into a meditative trance. But he couldn't shake the feeling something was wrong.

"Casey, he's in shock." He heard April say in panic as the two human's entered the lair.

"Set him down on the couch, Red." Casey said. "I'll get some blankets." Foot steps receded towards the dormitory. Splinter got up and approached the star way to the Dojo and peered out. April was sitting in one of the pit benches. Donatello was sprawled along it, his head resting on her lap. He wasn't visibly wounded, but April was clearly worried as she lightly stroked his cheek with the back of her fingers. Casey came back out of Raphael's room with a quilt and laid it over Donatello before pulling up one of the beanbag chairs and eyed the turtle with grave concern. The elder rat glanced about but didn't see his other sons.

"What are we gonna do about the guys?" Casey asked. "And what are we going to say to Splinter?"

"What has happened?!" Splinter demanded as he made his way to the pit, his orange eyes falling on his third eldest son in concern. Donatello appeared awake; however the mahogany brown irises of his eyes had retracted to the point where they were just small brown dots in a large field of white. His chest barely rose and fell with each breath. To Splinter he almost resembled a rag doll that had been tossed aside and forgotten. "Where are the others?!"

"They…they're gone…" Casey answered.

"Gone…?" Splinter asked, his heart squeezing at the word. It had just been scant months ago that he had been separated from his children. Wounded and alone he wondered for days, looking for a sign, a hope...that his sons were alive and safe. But the Shredder's words of "I took your son like I took your daughter" continued to burn and fester in his mind. With each passing day without his sons, each day he had to avoid the Foot Clan and the Kraang, each day he had to live like an animal. He slowly lost himself to his grief and to his mutation.

"Yeah they were with us one minute, and then this bolt of light appears taking Raph, Leo, and Mikey with it." Casey said as though he was trying to make the crazy story sound realistic. "The Foot Goons were distracted by what happened so April and I just grabbed Donnie and ran."

"I'm sorry Splinter." April said sadly. "I wish there was more Casey and I could have done, but the whole thing happened so fast." Splinter sighed sadly he moved into the pit. April respectfully got up, replacing her lap with one of the throw pillows and allowing Splinter to sit beside his remaining son. While he was glad to have one son at the very least, the absence of the others weighed heavily on the old rats heart.

* * *

In the following days, Donatello didn't speak to anyone nor did he eat or sleep. Often he would sit in his room or in the main room of the lair staring off into space, or drifted about the lair looking for his brothers. Other times he would try calling his brothers on his T-Phone, but only received a response saying that the number couldn't be reached. The action was heart breaking to watch, unfortunately there were also times he would act childishly as well.

Splinter had placed photos of Leonardo, Raphael, and Michelangelo at the shrine where he kept the image of his late wife and his lost daughter Miwa. However Donatello would often place all three images face down as though he couldn't accept that his brothers were gone. Splinter tried appeasing his distraught son by placing and image of the four brothers together happy and smiling. Unfortunately this image was also placed face down.

On one such morning Splinter was just setting down to a meditative trance when he heard the telltale click of a photo frame being placed down on the shelf surface.

"Donatello…" The elder rodent said as he opened one eye and glared at his remaining son. He didn't feel anger towards his son's actions, but he couldn't hide the irritation that this simple act was causing. "You need to accept that your brothers are gone!"

The purple masked turtle shook his head continuing to deny this truth. This saddened the Ninja Master greatly. He didn't want to accept that his three missing sons were gone as well; he prayed that they would magically return. And it was possible they could still be alive, but they could be trapped in another dimension, another time, or even in another existence and unable to return. But as the days of their absence increased, the more likely it was that they would never return.

Getting up Splinter approached his remaining son. He could see how the absence of the other turtles was affecting his brilliant son. The one boy that was one of them and yet stood apart from them, Donatello had built his entire being around his brothers and without them…he was lost. Calmly Splinter embraced his son, sharing his grief with Donatello. The two didn't say a word between them; they just silently acknowledged the void in their family that would never be filled.

* * *

Splinter however has his own issues with the disappearance of three of his four sons. He had become extremely protective of his last remaining son. Refusing to let Donatello leave the lair for any reason on the grounds that he was all the rodent master had left.

April and Casey would visit now and again to check on how Donnie and Splinter were fairing. April did acknowledge Splinter's reasons for not allowing Donnie to leave the lair…however she also felt such actions would also lead to more harm than good. She could see how lonely the tech savvy terrapin was without his brothers, and useless he felt being confined to the lair, particularly where the Foot Clan was concerned.

The Shredder had been over the moon with delight when he learned that three of the four Turtles had vanished. He wasted very little time gaining a foot hold in his attempts to gain control of the city by gaining dominion over the gangs of the city. The Purple Dragons stepped up their terrorism upon the innocent citizens of New York. Shredder hadn't forgotten about Splinter or Donatello, but he maintained that they would be flushed out of their sewer eventually and when they were they would be dealt with. The knowledge that all this was going on didn't sit well with the remaining Turtle or his human companions.

* * *

April entered the lair one such day and found Donnie without his mask sitting in front of the TV watching a news report about all that was going on in the city.

"Donnie…" April said as she approached Donnie. He was painfully thin and dark rings rested under his eyes, so dark they almost looked black. He didn't acknowledge her, his eyes were still trained on the news report.

"People are demanding to know, why isn't any one doing anything about this?" The pudgy multinational anchorman reported. "This is Carlos Chang O'Brian Gambe…Getting out of here."

Donatello didn't move or acknowledge when April turned the TV off. The only movement he made was jump slightly when April placed a hand on his shoulder.

"Donnie…" April said in concern. "Please talk to me?"

Donnie's brown eyes meet her concerned eyes. He opened is his mouth as though trying to say something, but nothing came out. Closing his eyes her brought his fists to his head as though doing so would be contain the rage of emotions that was flowing through his very being.

"You're letting your grief consume you…" April said as she wrapped her arms around him guiding his head to her shoulder. "Please just let it out…I don't know where the others went, nor when or even if they will be back. But what I do know is that they wouldn't want you to do this to do this to yourself. So please for my sake…please just let it out."

For a moment Donnie just rested in her arms like an oversized stuffed animal before a shudder passed through his body. A whimper followed until the only sound that resounded through the lair were his cries.

* * *

**Thank you to everyone who is reading this fic. **

**Any way I just wanted to quickly plug I'm helping to organize a Fan Fic challenge. This challenge was started by Crazy Fangirl 14 on the stealthystories forum. **

**The challenge is for tmnt fanfic authors to write a short story based on a TMNT fic another author has written. **

**Further details for this challenge can be found here. **** tmntficchallenges dot blogspot dot com/**


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